Discrete Global Grid System is a new data model which supports the fusion processing of multi-source spatial data. The Fourier Transform connects spatial domain and frequency domain which is significant to the enhancement of remote sensing image based on grid system. According to the subdivision scheme of aperture 3 hexagonal grid, a regular hexagonal structure is designed in this paper. The two-dimensional discrete Fourier on this structure can be transformed into one-dimensional transform which can be accelerated by Cooley-Tukey algorithm. A remote-sensing image is used to verify the proposed method. The experimental result shows the Fast Fourier Transformation investigated in this paper is correct and efficient with a complexity of N log_2N, with the increase of data, the efficiency will grow in an exponential manner.